def test_sum_labels():
labels = np.array([[1, 2], [2, 4]], np.int8)
for type in types:
input = np.array([[1, 2], [3, 4]], type)
output_sum = ndimage.sum(input, labels=labels, index=[4, 8, 2])
output_labels = ndimage.sum_labels(
input, labels=labels, index=[4, 8, 2])
assert (output_sum == output_labels).all()
assert_array_almost_equal(output_labels, [4.0, 0.0, 5.0])
def _counting_filter_cpu(
image,
threshold=5,
integrate=False,
hdr_mask=None,
method="maximum",
mean_electron_val=256,
):
"""This counting filter is GPU designed so that you can apply an hdr mask
for regions of the data that are higher than some predetermined threshold.
It also allows for you to integrate the electron events rather than counting
them.
"""
tick = time.time()
nav_dims = len(image.shape) - 2
try:
if hdr_mask is not None:
hdr_img = image * hdr_mask
hdr_img = hdr_img / mean_electron_val
nav_slice = slice(None) * nav_dims
if nav_slice == ():
image[hdr_mask] = 0
else:
image[nav_slice, hdr_img] = 0
thresh = image > threshold
struct = np.zeros((3, ) * (nav_dims + 2))
if nav_dims == ():
struct = 1
else:
struct[(1, ) * nav_dims] = 1
all_labels, num = label(thresh, structure=struct) # get blobs
print("Number of electrons Found! : ", num, flush=True)
if method is "center_of_mass":
ind = center_of_mass(image, all_labels, range(1, num))
elif method is "maximum":
ind = maximum_position(image, all_labels, range(1, num))
ind = np.rint(ind).astype(int)
x = np.zeros(shape=image.shape)
if integrate:
try:
image[~threshold] = 0
sum_lab = sum_labels(image, all_labels, range(1, num))
inds = (i for i in ind)
x[inds] = sum_lab
except:
pass
else:
try:
inds = (i for i in ind)
x[inds] = 1
except:
pass
if hdr_mask is not None:
if nav_slice == ():
image[hdr_mask] = hdr_img[hdr_mask]
else:
image[nav_slice, hdr_mask] = hdr_img[nav_slice, hdr_mask]
if integrate is False and hdr_mask is None:
x = x.astype(bool) # converting to boolean...
tock = time.time()
_logger.info(msg="Time elapsed for one Chunk" + str(tock - tick) +
" seconds")
return x
except MemoryError:
_logger.error("Failed.... Memory Error")